In The Plateau, Secretary Bishop clarifies to him that they need to embed Bolivia Dunham's memory in Olivia to make her a more willing experimental subject and ultimately, to learn how to crossover to this universe without any dangerous consequences (The Plateau).

In The Abducted, continues the conspiracy with Secretary Bishop to manipulate Olivia while leading the effort capture The Candy Man, a criminal who has committed atrocities against children - including Broyles own son.

In Entrada, Broyles is murdered for helping Olivia cross back into her own universe. When Bolivia is transported back to the alternate universe, she is replaced in our universe by the badly burned and maimed Broyles.

In Immortality, Bolivia Dunham tells her boyfriend Frank that Fringe Division is unable to find any leads on Broyles disappearance and that his car was found at the edge of a 'No-Go' security zone.

In One Night In October, restored to the alternate universe in the timeline that lacked Walter's, Olivia's and Peter's interference, the Colonel tasks his team and the visiting Olivia to locate psychopathic serial killer that is cryogenically stealing the pleasant memories of those he abducts, leaving them dead.

In Back To Where You've Never Been, oversees the investigation of the trans-universal incursion at the opera house in Brooklyn. He allows his team to follow a lead to David Jones secret lab, then calls Jones to let him know that his Fringe agents are heading his way.

In Enemy Of My Enemy, continues to hide his conspiratorial agenda from his colleagues, then abets Jones' evasion from authorities.

In Making Angels, he deploys Bolivia to retrieve Agent Farnsworth when she crosses at Liberty Island without permission.

In Everything In Its Right Place, he receives information on the vigilante shapeshifter, then informs Nina Sharp so she can have the errant shapeshifter assassinated.

In The Consultant, accepts medication from David Robert Jones to save his son's life, then renegs on his agreement to destroy the trans-universal bridge on Liberty Island. He accepts his fate as a collaborater and surrenders to Fringe Division on this side of the bridge.

"What about the other victim? Did the bus driver see her get on too? Were they not together? ...I'm confused." - to Olivia Dunham (overlapping universes have them speaking to one another as if they are addressing their original colleagues) (The Road Not Taken)

"Okay people, nap time's over. Let's go to work." - to his Fringe Division staff manning the Situation Room (responding to the Class One breach in-progress in nearby Brooklyn as the Science Team infiltrates the parallel universe) (Over There, Part 1)

"Alright, people, let's move. This is not a drill." - to his Fringe Division staff manning the Situation Room (responding to the Directive issued by DoD Secretary Bishop to find fugitive Doctor Walter Bishop before he can exfilitrate back to this universe) (Over There, Part 2)

"I think from what I know of Olivia Dunham. She's the one person I would bet on who could survive." - to Secretary Bishop (betting on the come that either universe's Dunham has the tenacity and survival skills to escape her Liberty Island imprisonment and swim the frigid Manhatan waters to evade her captors) (Olivia)

"Putting an impostor on my team is too big a risk. Now, you can run all the tests you want, but you don't know how this Olivia will respond in the field." - to Secretary Bishop (reticent about the plan to manipulate the visiting Fringe Agent to win the war between universes) (The Plateau)

"What I'm about to tell you is classified. The people entombed in Amber are in a state of suspended animation." - to Olivia and Lincoln Lee (sharing a well kept and little known fact about the product being used to seal the rift between universes) (Amber 31422)

"Dunham... the F.B.I. ceased to exist over a decade ago... at least on this side it did. You know who you are, don't you?" - to Olivia Dunham (with a hint of protective mentorship. letting her in on the State secret she suspected she knew) (The Abducted)

"Subcutaneous tracker. I'm too important to lose. Look, I've seen war. But if what you're saying is true, In the end, I have to believe in hope. Please make this worth it. Go!" - to Olivia Dunham (his last words to her after abetting her escape from captivity and helping her return to this universe. considered a traitor by Secretary Bishop for this act, he was dismembered and his burned corpse sent to this universe in a spatial trade-off to extract Bolivia Dunham from her espionage mission) (Entrada)

" If you're right, Agent Dunham, then finding Professor McClennan is our best chance to save Noreen Miller. Let me know when you have something." - to his assembled team, as well (willing to go out on a limb and deploy assets like McClennan from this universe to stop the serial killer in his universe) (One Night In October)

"Mister Secretary, it's Colonel Broyles. Sorry to disturb you, but you need to know there's been an incursion from the other universe. We've apprehended two men who were on their way to you. One is their Fringe Division's Lincoln Lee. The other man... he claims to be Peter Bishop, your son." - to Secretary Bishop (with info that might not come as news to a father that had recently tried to lure his offspring home in a parallel timeline) (Back To Where You've Never Been)

"All units, move into the plaza and maintain a visual on the target." - to all Fringe personnel pursuing David Robert Jones (over the tactical radios. while he waits as an accomplice in a nearby alley for Jones to quietly escape capture before his eyes) (Enemy Of My Enemy)

"We don't know. She went off the grid immediately after crossing over. Alright. Let's send a team of agents to retrieve her." - to his situation room staff (Olivia takes the call to duty and volunteers to retrieve Agent Farnsworth from her personal quest to spend time with her counterpart - Astrid) (Making Angels)

"Captain Lee, assemble a TAC Team. And keep me apprised of the situation." - to Captain Lincoln (his final conversation with his prized top officer before Lee is assassinated by a sniper) (Everything In Its Right Place)

"I buried an agent today. A good man. And I’m also well aware that Agent Lee isn't the first casualty of our... collaboration. Some day I’ll have to account for what I’ve done." - to David Robert Jones (satisfied that he has done what he has needed to do to medically mend his child. dissatisfied that he has had to make a deal with the Devil along the way) (The Consultant)

"Doctor Bishop. May I ask you something? If you had to do it all over again, would you make the same choice?" - to Walter, in the presence of Bolivia Dunham (second-guessing the tenuous ethical path he has chosen in this particular timeline. hours before crossings the bridge on Liberty Island and remanding himself to the custody of Phillip Broyles in this universe) (The Consultant)